How the vertebrates were made: selective pruning of a double-duplicated genome

Vertebrates are the result of an ancient double duplication of the genome. A new study published in BMC Biology explores the selective retention of genes after this event, finding an extensive enrichment of signaling proteins and transcription factors. Analysis of their expression patterns, interactions and subsequent history reflect the forces that drove their evolution, and with it the evolution of vertebrate complexity

Transport criticality in triangular lattice Hubbard model

We study electric transport near the Mott metal-insulator transition. Optical conductivity of the half-filled Hubbard model on a triangular lattice is calculated based on a cellular dynamical mean field theory including vertex corrections inside the cluster. By investigating the spectrum at low frequencies, we find that a Drude peak on the metallic side smoothly connects to an "ingap" peak on the insulating side. The optical weight of these peaks exhibits a critical behavior with power-law near the Mott critical end point, $|D-D^*|\propto|U-U^*|^{1/\delta}$. We find that the critical exponent $1/\delta$ differs from the exponents in the thermodynamics.Comment: 4 pages, 4 figure

The heterogeneous coma of comet 67P/Churyumov-Gerasimenko as seen by ROSINA: H <inf>2</inf> O, CO <inf>2</inf>, and CO from September 2014 to February 2016

Context. The ESA Rosetta mission has been investigating the environment of comet 67P/Churyumov-Gerasimenko (67P) since August 2014. Among the experiments on board the spacecraft, the ROSINA experiment (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) includes two mass spectrometers to analyse the composition of neutrals and ions and a COmet Pressure Sensor (COPS) to monitor the density and velocity of neutrals in the coma. Aims. We study heterogeneities in the coma during three periods starting in October 2014 (summer in the northern hemisphere) and ending in February 2016 (end of winter in the northern hemisphere). We provide a detailed description of the main volatiles dynamics (H2O, CO2, CO) and their abundance ratios. Methods. We analysed and compared the data of the Reflectron-Type Time-Of-Flight (RTOF) mass spectrometer with data from both the Double Focusing Mass Spectrometer (DFMS) and COPS during the comet escort phase. This comparison has demonstrated that the observations performed with each ROSINA sensor are indeed consistent. Furthermore, we used a Direct Simulation Monte Carlo (DSMC) model to compare modelled densitites with in situ detections. Results. Our analysis shows how the active regions of the main volatiles evolve with the seasons with a variability mostly driven by the illumination conditions; this is the case except for an unexpected dichotomy suggesting the presence of a dust layer containing water deposited in the northern hemisphere during previous perihelions hiding the presence of CO2. The influence of various parameters is investigated in detail: distance to the comet, heliocentric distance, longitude and latitude of sub-satellite point, local time, and phase angle

The Evolution of a High Copy Gene Array in Arabidopsis

Local gene duplication is a prominent mechanism of gene copy number expansion. Elucidating the mechanisms by which local duplicates arise is necessary in understanding the evolution of genomes and their host organisms. Chromosome one of Arabidopsis thaliana contains an 81-gene array subdivided into 27 triplet units (t-units), with each t-unit containing three pre-transfer RNA genes. We utilized phylogenetic tree reconstructions and comparative genomics to order the events leading to the array’s formation, and propose a model using unequal crossing-over as the primary mechanism of array formation. The model is supported by additional phylogenetic information from intergenic spacer sequences separating each t-unit, comparative analysis to an orthologous array of 12 t-units in the sister taxa Arabidopsis lyrata, and additional modeling using a stochastic simulation of orthologous array divergence. Lastly, comparative phylogenetic analysis demonstrates that the two orthologous t-unit arrays undergo concerted evolution within each taxa and are likely fluctuating in copy number under neutral evolutionary drift. These findings hold larger implications for future research concerning gene and genome evolution

Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

Bacteria glide across solid surfaces by mechanisms that have remained largely mysterious despite decades of research. In the deltaproteobacterium Myxococcus xanthus, this locomotion allows the formation stress-resistant fruiting bodies where sporulation takes place. However, despite the large number of genes identified as important for gliding, no specific machinery has been identified so far, hampering in-depth investigations. Based on the premise that components of the gliding machinery must have co-evolved and encode both envelope-spanning proteins and a molecular motor, we re-annotated known gliding motility genes and examined their taxonomic distribution, genomic localization, and phylogeny. We successfully delineated three functionally related genetic clusters, which we proved experimentally carry genes encoding the basal gliding machinery in M. xanthus, using genetic and localization techniques. For the first time, this study identifies structural gliding motility genes in the Myxobacteria and opens new perspectives to study the motility mechanism. Furthermore, phylogenomics provide insight into how this machinery emerged from an ancestral conserved core of genes of unknown function that evolved to gliding by the recruitment of functional modules in Myxococcales. Surprisingly, this motility machinery appears to be highly related to a sporulation system, underscoring unsuspected common mechanisms in these apparently distinct morphogenic phenomena

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

Background: The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC endsequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species. Results: We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies. Conclusions: Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome. (Résumé d'auteur

Sulphur-bearing species in the coma of comet 67P/Churyumov–Gerasimenko

Several sulphur-bearing species have already been observed in different families of comets. However, the knowledge on the minor sulphur species is still limited. The comet’s sulphur inventory is closely linked to the pre-solar cloud and holds important clues to the degree of reprocessing of the material in the solar nebula and during comet accretion. Sulphur in pre-solar clouds is highly depleted, which is quite puzzling as the S/O ratio in the diffuse interstellar medium is cosmic. This work focuses on the abundance of the previously known species H2S, OCS, SO, S2, SO2 and CS2 in the coma of comet 67P/Churyumov–Gerasimenko measured by Rosetta Orbiter Spectrometer for Ion and Neutral Analysis/Double Focusing Mass Spectrometer between equinox and perihelion 2015. Furthermore, we present the first detection of S3, S4, CH3SH and C2H6S in a comet, and we determine the elemental abundance of S/O in the bulk ice of (1.47 ± 0.05) × 10−2. We show that SO is present in the coma originating from the nucleus, but not CS in the case of 67P, and for the first time establish that S2 is present in a volatile and a refractory phase. The derived total elemental sulphur abundance of 67P is in agreement with solar photospheric elemental abundances and shows no sulphur depletion as reported for dense interstellar clouds. Also the presence of S2 at heliocentric distances larger than 3 au indicates that sulphur-bearing species have been processed by radiolysis in the pre-solar cloud and that at least some of the ice from this cloud has survived in comets up the present